PMID- 19014460 OWN - NLM STAT- PubMed-not-MEDLINE DCOM- 20090723 LR - 20220318 IS - 1755-8794 (Electronic) IS - 1755-8794 (Linking) VI - 1 DP - 2008 Nov 11 TI - Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries. PG - 56 LID - 10.1186/1755-8794-1-56 [doi] AB - BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies in humans. The average 5-year survival rate is one of the lowest among aggressive cancers, showing no significant improvement in recent years. When detected early, HNSCC has a good prognosis, but most patients present metastatic disease at the time of diagnosis, which significantly reduces survival rate. Despite extensive research, no molecular markers are currently available for diagnostic or prognostic purposes. METHODS: Aiming to identify differentially-expressed genes involved in laryngeal squamous cell carcinoma (LSCC) development and progression, we generated individual Serial Analysis of Gene Expression (SAGE) libraries from a metastatic and non-metastatic larynx carcinoma, as well as from a normal larynx mucosa sample. Approximately 54,000 unique tags were sequenced in three libraries. RESULTS: Statistical data analysis identified a subset of 1,216 differentially expressed tags between tumor and normal libraries, and 894 differentially expressed tags between metastatic and non-metastatic carcinomas. Three genes displaying differential regulation, one down-regulated (KRT31) and two up-regulated (BST2, MFAP2), as well as one with a non-significant differential expression pattern (GNA15) in our SAGE data were selected for real-time polymerase chain reaction (PCR) in a set of HNSCC samples. Consistent with our statistical analysis, quantitative PCR confirmed the upregulation of BST2 and MFAP2 and the downregulation of KRT31 when samples of HNSCC were compared to tumor-free surgical margins. As expected, GNA15 presented a non-significant differential expression pattern when tumor samples were compared to normal tissues. CONCLUSION: To the best of our knowledge, this is the first study reporting SAGE data in head and neck squamous cell tumors. Statistical analysis was effective in identifying differentially expressed genes reportedly involved in cancer development. The differential expression of a subset of genes was confirmed in additional larynx carcinoma samples and in carcinomas from a distinct head and neck subsite. This result suggests the existence of potential common biomarkers for prognosis and targeted-therapy development in this heterogeneous type of tumor. FAU - Silveira, Nelson J F AU - Silveira NJ AD - Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraiba, UNIVAP, Sao Jose dos Campos, SP, Brazil. nelsonjfs@univap.br FAU - Varuzza, Leonardo AU - Varuzza L FAU - Machado-Lima, Ariane AU - Machado-Lima A FAU - Lauretto, Marcelo S AU - Lauretto MS FAU - Pinheiro, Daniel G AU - Pinheiro DG FAU - Rodrigues, Rodrigo V AU - Rodrigues RV FAU - Severino, Patricia AU - Severino P FAU - Nobrega, Francisco G AU - Nobrega FG CN - Head and Neck Genome Project GENCAPO FAU - Silva, Wilson A Jr AU - Silva WA Jr FAU - de B Pereira, Carlos A AU - de B Pereira CA FAU - Tajara, Eloiza H AU - Tajara EH LA - eng PT - Journal Article DEP - 20081111 PL - England TA - BMC Med Genomics JT - BMC medical genomics JID - 101319628 PMC - PMC2629771 FIR - Curry, P M IR - Curry PM FIR - de Carvalho, M B IR - de Carvalho MB FIR - Dias-Neto, E IR - Dias-Neto E FIR - Figueiredo, D L A IR - Figueiredo DL FIR - Fukuyama, E E IR - Fukuyama EE FIR - Gois-Filho, J F IR - Gois-Filho JF FIR - Leopoldino, A M IR - Leopoldino AM FIR - Mamede, R C M IR - Mamede RC FIR - Michaluart-Junior, P IR - Michaluart-Junior P FIR - Moreira-Filho, C A IR - Moreira-Filho CA FIR - Moyses, R A IR - Moyses RA FIR - Nobrega, F G IR - Nobrega FG FIR - Nobrega, M P IR - Nobrega MP FIR - Nunes, F D IR - Nunes FD FIR - Ojopi, E P B IR - Ojopi EP FIR - Okamoto, O K IR - Okamoto OK FIR - Serafini, L N IR - Serafini LN FIR - Severino, P IR - Severino P FIR - Silva, A M A IR - Silva AM FIR - Silva, W A Jr IR - Silva WA Jr FIR - Silveira, N J F IR - Silveira NJ FIR - Souza, S C O M IR - Souza SC FIR - Tajara, E H IR - Tajara EH FIR - Wunsch-Filho, V IR - Wunsch-Filho V FIR - Zago, M A IR - Zago MA FIR - Amar, A IR - Amar A FIR - Arap, S S IR - Arap SS FIR - Araujo, N S S IR - Araujo NS FIR - Araujo-Filho, V IR - Araujo-Filho V FIR - Barbieri, R B IR - Barbieri RB FIR - Bandeira, C M IR - Bandeira CM FIR - Bastos, A U IR - Bastos AU FIR - Braconi, M A IR - Braconi MA FIR - Brandao, L G IR - Brandao LG FIR - Brandao, R M IR - Brandao RM FIR - Canto, A L IR - Canto AL FIR - Carmona-Raphe, J IR - Carmona-Raphe J FIR - Carvalho-Neto, P B IR - Carvalho-Neto PB FIR - Casemiro, A F IR - Casemiro AF FIR - Cerione, M IR - Cerione M FIR - Cernea, C R IR - Cernea CR FIR - Cicco, R IR - Cicco R FIR - Chagas, M J IR - Chagas MJ FIR - Chedid, H IR - Chedid H FIR - Chiappini, P B O IR - Chiappini PB FIR - Correia, L A IR - Correia LA FIR - Costa, A IR - Costa A FIR - Costa, A C W IR - Costa AC FIR - Cunha, B R IR - Cunha BR FIR - Curioni, O A IR - Curioni OA FIR - Dias, T H G IR - Dias TH FIR - Durazzo, M IR - Durazzo M FIR - Ferraz, A R IR - Ferraz AR FIR - Figueiredo, R O IR - Figueiredo RO FIR - Fortes, C S IR - Fortes CS FIR - Franzi, S A IR - Franzi SA FIR - Frizzera, A P Z IR - Frizzera AP FIR - Gallo, J IR - Gallo J FIR - Gazito, D IR - Gazito D FIR - Guimaraes, P E M IR - Guimaraes PE FIR - Gutierres, A P IR - Gutierres AP FIR - Inamine, R IR - Inamine R FIR - Kaneto, C M IR - Kaneto CM FIR - Lehn, C N IR - Lehn CN FIR - Lopez, R V M IR - Lopez RV FIR - Macarenco, R IR - Macarenco R FIR - Magalhaes, R P IR - Magalhaes RP FIR - Martins, A E IR - Martins AE FIR - Meneses, C IR - Meneses C FIR - Mercante, A M C IR - Mercante AM FIR - Montenegro, F L M IR - Montenegro FL FIR - Pinheiro, D G IR - Pinheiro DG FIR - Polachini, G M IR - Polachini GM FIR - Porsani, A F IR - Porsani AF FIR - Rapoport, A IR - Rapoport A FIR - Rodini, C O IR - Rodini CO FIR - Rodrigues, A N IR - Rodrigues AN FIR - Rodrigues-Lisoni, F C IR - Rodrigues-Lisoni FC FIR - Rodrigues, R V IR - Rodrigues RV FIR - Rossi, L IR - Rossi L FIR - Santos, A R D IR - Santos AR FIR - Santos, M IR - Santos M FIR - Settani, F IR - Settani F FIR - Silva, F A M IR - Silva FA FIR - Silva, I T IR - Silva IT FIR - Silva-Filho, G B IR - Silva-Filho GB FIR - Smith, R B IR - Smith RB FIR - Souza, T B IR - Souza TB FIR - Stabenow, E IR - Stabenow E FIR - Takamori, J T IR - Takamori JT FIR - Tavares, M R IR - Tavares MR FIR - Turcano, R IR - Turcano R FIR - Valentim, P J IR - Valentim PJ FIR - Vidotto, A IR - Vidotto A FIR - Volpi, E M IR - Volpi EM FIR - Xavier, F C A IR - Xavier FC FIR - Yamagushi, F IR - Yamagushi F FIR - Cominato, M L IR - Cominato ML FIR - Correa, P M S IR - Correa PM FIR - Mendes, G S IR - Mendes GS FIR - Paiva, R IR - Paiva R FIR - Ramos, O IR - Ramos O FIR - Silva, C IR - Silva C FIR - Silva, M J IR - Silva MJ FIR - Tarla, M V C IR - Tarla MV EDAT- 2008/11/19 09:00 MHDA- 2008/11/19 09:01 PMCR- 2008/11/11 CRDT- 2008/11/19 09:00 PHST- 2008/03/27 00:00 [received] PHST- 2008/11/11 00:00 [accepted] PHST- 2008/11/19 09:00 [pubmed] PHST- 2008/11/19 09:01 [medline] PHST- 2008/11/19 09:00 [entrez] PHST- 2008/11/11 00:00 [pmc-release] AID - 1755-8794-1-56 [pii] AID - 10.1186/1755-8794-1-56 [doi] PST - epublish SO - BMC Med Genomics. 2008 Nov 11;1:56. doi: 10.1186/1755-8794-1-56.